derekson -- I think there's one misconception in your post, which is that positional adjustments are calculated relative to average
offense at each position. Unless I'm badly misreading FG's explanations (
here, for instance), they are calculated relative to average
defense. I.e., a LF is worth 10 runs less than a CF because an average defensive LF would be about a -10 defensive CF).
The -5 adjustment for DHs is based on the observation that DHs when they do play 1B tend to be about that bad (actually, according to Cameron's comment
here, they tend to be about -10 first basemen, but the adjustment gives them back 5 runs for the difficulty of hitting as a DH).
You could call this "penalizing" DHs, but what's the alternative? The positional adjustments are there for a reason, and there has to be one for DH, and I don't see a better way to do it. (The exact values are another story, and may be fair game for critique.) It's a good common-sense observation that DHs are probably worse than average fielders even at the easiest position on the field, because if they weren't, they would in most cases be out there on the field.